Contacts of the strand formed by residues 38 - 45 (chain D) in PDB entry 4CDC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439C LEU* 3.2 39.5 + - + +
17D PHE 3.8 0.5 - - - +
18D GLN* 3.5 9.5 - - - +
19D VAL* 3.0 39.3 + - + +
22D SER* 6.6 0.2 - - - -
36D GLN 3.9 0.2 - - - -
37D GLU* 1.3 85.0 - - + +
39D LYS* 1.3 71.2 + - - +
40D VAL* 3.8 16.4 - - + -
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Residues in contact with LYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D VAL* 3.7 34.5 - - + -
17D PHE 3.7 2.9 - - - -
18D GLN* 3.9 19.5 - - - +
38D LYS* 1.3 85.6 - - - +
40D VAL* 1.3 66.7 + - - +
41D VAL* 4.2 17.2 - - + +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C LEU* 4.1 20.0 - - + +
15D TRP 4.0 0.5 - - - +
16D VAL* 3.7 0.5 - - - -
17D PHE* 2.8 42.5 + - + +
19D VAL* 4.3 12.3 - - + -
38D LYS* 3.8 17.7 - - + -
39D LYS* 1.3 80.1 - - - +
41D VAL* 1.3 72.0 + - - +
42D VAL* 4.1 14.5 + - + -
52D ASP* 5.7 3.6 - - + -
72D LEU* 6.2 0.2 - - + -
77D TRP* 4.2 23.6 - - + -
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D THR* 3.7 28.5 - - + -
15D TRP 3.5 6.3 - - - +
16D VAL* 4.5 13.0 - - + -
39D LYS* 4.2 24.4 + - + +
40D VAL* 1.3 76.2 - - - +
42D VAL* 1.3 71.1 + - - +
43D TYR* 3.9 20.6 - - + +
52D ASP* 3.8 20.3 - - - +
53D ASP* 3.5 22.1 + - - +
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Residues in contact with VAL 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLY 3.9 0.7 - - - +
14D THR* 3.6 1.6 - - - +
15D TRP* 2.8 37.6 + - + +
17D PHE* 4.2 25.6 - - + -
40D VAL* 4.1 16.4 + - + -
41D VAL* 1.3 81.0 - - - +
43D TYR* 1.3 67.3 + - - +
44D LEU* 3.7 24.9 - - + -
50D ALA* 4.4 3.1 - - + -
51D TYR 3.5 10.3 - - - +
52D ASP* 5.1 0.2 - - + -
70D ILE* 4.4 8.7 - - + -
72D LEU* 3.9 26.9 - - + -
77D TRP* 5.2 5.4 - - - +
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Residues in contact with TYR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLY 3.5 4.9 - - - +
14D THR* 3.2 36.6 - - + -
41D VAL* 3.9 15.4 - - + +
42D VAL* 1.3 74.7 - - - +
44D LEU* 1.3 61.9 - - - +
45D GLN* 4.1 2.9 - - + +
49D THR 3.9 0.7 - - - +
50D ALA* 3.3 4.9 - - - -
51D TYR* 2.8 84.7 + + + -
52D ASP* 4.2 8.5 - - - -
53D ASP* 2.6 33.4 + - - -
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.6 47.8 - - + +
12D LEU* 3.4 7.6 - - - +
13D GLY* 2.9 33.8 + - - +
15D TRP* 3.8 15.5 - - + -
42D VAL* 3.7 15.0 - - + -
43D TYR* 1.3 80.0 - - - +
45D GLN* 1.3 64.0 + - - +
49D THR 3.6 1.8 - - - -
50D ALA* 3.6 22.9 - - + -
60D PHE* 3.8 24.5 - - + -
68D PHE* 5.4 0.7 - - + -
70D ILE* 4.0 22.2 - - + -
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.5 5.6 - - - -
43D TYR* 5.1 1.9 - - + +
44D LEU* 1.3 79.6 - - - +
46D LYS* 1.3 60.7 + - - +
49D THR* 2.9 35.4 + - - +
51D TYR* 3.1 30.6 + - + -
60D PHE* 3.3 4.0 - - - -
332H ASN* 3.1 37.0 - - + +
333H GLU* 2.9 36.5 + - - +
334H ALA* 3.1 12.9 + - - +
420I GLY* 5.6 2.8 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il